• using R Under development (unstable) (2024-09-05 r87099)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     clang version 18.1.8     flang-new version 18.1.8
• running under: Fedora Linux 36 (Workstation Edition)
• using session charset: UTF-8
• using option ‘--no-stop-on-test-error’
• checking for file ‘dotwhisker/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘dotwhisker’ version ‘0.8.2’
• package encoding: UTF-8
• checking package namespace information ... OK
• checking package dependencies ... OK
• checking if this is a source package ... OK
• checking if there is a namespace ... OK
• checking for executable files ... OK
• checking for hidden files and directories ... OK
• checking for portable file names ... OK
• checking for sufficient/correct file permissions ... OK
• checking whether package ‘dotwhisker’ can be installed ... [12s/38s] OK See the install log for details.
• checking installed package size ... OK
• checking package directory ... OK
• checking ‘build’ directory ... OK
• checking DESCRIPTION meta-information ... OK
• checking top-level files ... OK
• checking for left-over files ... OK
• checking index information ... OK
• checking package subdirectories ... OK
• checking code files for non-ASCII characters ... OK
• checking R files for syntax errors ... OK
• checking whether the package can be loaded ... [5s/17s] OK
• checking whether the package can be loaded with stated dependencies ... [5s/13s] OK
• checking whether the package can be unloaded cleanly ... [5s/11s] OK
• checking whether the namespace can be loaded with stated dependencies ... OK
• checking whether the namespace can be unloaded cleanly ... [5s/10s] OK
• checking loading without being on the library search path ... OK
• checking use of S3 registration ... OK
• checking dependencies in R code ... OK
• checking S3 generic/method consistency ... OK
• checking replacement functions ... OK
• checking foreign function calls ... OK
• checking R code for possible problems ... [28s/87s] OK
• checking Rd files ... OK
• checking Rd metadata ... OK
• checking Rd line widths ... OK
• checking Rd cross-references ... OK
• checking for missing documentation entries ... OK
• checking for code/documentation mismatches ... OK
• checking Rd \usage sections ... OK
• checking Rd contents ... OK
• checking for unstated dependencies in examples ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [12s/46s] ERROR Running examples in ‘dotwhisker-Ex.R’ failed The error most likely occurred in: > ### Name: small_multiple > ### Title: Generate a 'Small Multiple' Plot of Regression Results > ### Aliases: small_multiple > > ### ** Examples > > library(broom) > library(dplyr) Attaching package: ‘dplyr’ The following objects are masked from ‘package:stats’:     filter, lag The following objects are masked from ‘package:base’:     intersect, setdiff, setequal, union > > # Generate a tidy data frame of regression results from six models > > m <- list() > ordered_vars <- c("wt", "cyl", "disp", "hp", "gear", "am") > m[[1]] <- lm(mpg ~ wt, data = mtcars) > m123456_df <- m[[1]] %>% tidy %>% by_2sd(mtcars) %>% + mutate(model = "Model 1") > > for (i in 2:6) { + m[[i]] <- update(m[[i-1]], paste(". ~ . +", ordered_vars[i])) + m123456_df <- rbind(m123456_df, m[[i]] %>% tidy %>% by_2sd(mtcars) %>% + mutate(model = paste("Model", i))) + } > > # Generate a 'small multiple' plot > small_multiple(m123456_df) Error in `$<-.data.frame`(`*tmp*`, "x_ind", value = c(1L, 1L, 1L, 1L, :   replacement has 36 rows, data has 37 Calls: small_multiple -> $<- -> $<-.data.frame Execution halted
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [41s/114s] ERROR Error(s) in re-building vignettes: --- re-building ‘dotwhisker-vignette.Rmd’ using rmarkdown ** Processing: /data/gannet/ripley/R/packages/tests-clang/dotwhisker.Rcheck/vign_test/dotwhisker/vignettes/dotwhisker-vignette_files/figure-html/basic-1.png 288x288 pixels, 8 bits/pixel, 255 colors in palette Input IDAT size = 2121 bytes Input file size = 2976 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 1854   zc = 9 zm = 8 zs = 1 f = 0   zc = 1 zm = 8 zs = 2 f = 0   zc = 9 zm = 8 zs = 3 f = 0   zc = 9 zm = 8 zs = 0 f = 5   zc = 9 zm = 8 zs = 1 f = 5   zc = 1 zm = 8 zs = 2 f = 5   zc = 9 zm = 8 zs = 3 f = 5                                 Selecting parameters:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 1854 Output IDAT size = 1854 bytes (267 bytes decrease) Output file size = 2709 bytes (267 bytes = 8.97% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang/dotwhisker.Rcheck/vign_test/dotwhisker/vignettes/dotwhisker-vignette_files/figure-html/ci-1.png 288x288 pixels, 8 bits/pixel, 253 colors in palette Input IDAT size = 2458 bytes Input file size = 3307 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 1927   zc = 9 zm = 8 zs = 1 f = 0   zc = 1 zm = 8 zs = 2 f = 0   zc = 9 zm = 8 zs = 3 f = 0   zc = 9 zm = 8 zs = 0 f = 5   zc = 9 zm = 8 zs = 1 f = 5   zc = 1 zm = 8 zs = 2 f = 5   zc = 9 zm = 8 zs = 3 f = 5                                 Selecting parameters:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 1927 Output IDAT size = 1927 bytes (531 bytes decrease) Output file size = 2776 bytes (531 bytes = 16.06% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang/dotwhisker.Rcheck/vign_test/dotwhisker/vignettes/dotwhisker-vignette_files/figure-html/multipleModels-1.png 288x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 11194 bytes Input file size = 11284 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 8025   zc = 9 zm = 8 zs = 1 f = 0   zc = 1 zm = 8 zs = 2 f = 0   zc = 9 zm = 8 zs = 3 f = 0   zc = 9 zm = 8 zs = 0 f = 5   zc = 9 zm = 8 zs = 1 f = 5   zc = 1 zm = 8 zs = 2 f = 5   zc = 9 zm = 8 zs = 3 f = 5                                 Selecting parameters:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 8025 Output IDAT size = 8025 bytes (3169 bytes decrease) Output file size = 8103 bytes (3181 bytes = 28.19% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang/dotwhisker.Rcheck/vign_test/dotwhisker/vignettes/dotwhisker-vignette_files/figure-html/intercept-1.png 288x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 11006 bytes Input file size = 11096 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 8248   zc = 9 zm = 8 zs = 1 f = 0   zc = 1 zm = 8 zs = 2 f = 0   zc = 9 zm = 8 zs = 3 f = 0   zc = 9 zm = 8 zs = 0 f = 5   zc = 9 zm = 8 zs = 1 f = 5   zc = 1 zm = 8 zs = 2 f = 5   zc = 9 zm = 8 zs = 3 f = 5                                 Selecting parameters:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 8248 Output IDAT size = 8248 bytes (2758 bytes decrease) Output file size = 8326 bytes (2770 bytes = 24.96% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang/dotwhisker.Rcheck/vign_test/dotwhisker/vignettes/dotwhisker-vignette_files/figure-html/ggplot-1.png 288x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 9157 bytes Input file size = 9247 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6818   zc = 9 zm = 8 zs = 1 f = 0   zc = 1 zm = 8 zs = 2 f = 0   zc = 9 zm = 8 zs = 3 f = 0   zc = 9 zm = 8 zs = 0 f = 5   zc = 9 zm = 8 zs = 1 f = 5   zc = 1 zm = 8 zs = 2 f = 5   zc = 9 zm = 8 zs = 3 f = 5                                 Selecting parameters:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6818 Output IDAT size = 6818 bytes (2339 bytes decrease) Output file size = 6896 bytes (2351 bytes = 25.42% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang/dotwhisker.Rcheck/vign_test/dotwhisker/vignettes/dotwhisker-vignette_files/figure-html/tidyData-1.png 288x288 pixels, 8 bits/pixel, 254 colors in palette Input IDAT size = 2126 bytes Input file size = 2978 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 1866   zc = 9 zm = 8 zs = 1 f = 0   zc = 1 zm = 8 zs = 2 f = 0   zc = 9 zm = 8 zs = 3 f = 0   zc = 9 zm = 8 zs = 0 f = 5   zc = 9 zm = 8 zs = 1 f = 5   zc = 1 zm = 8 zs = 2 f = 5   zc = 9 zm = 8 zs = 3 f = 5                                 Selecting parameters:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 1866 Output IDAT size = 1866 bytes (260 bytes decrease) Output file size = 2718 bytes (260 bytes = 8.73% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang/dotwhisker.Rcheck/vign_test/dotwhisker/vignettes/dotwhisker-vignette_files/figure-html/tidy-1.png 288x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 10170 bytes Input file size = 10260 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7144   zc = 9 zm = 8 zs = 1 f = 0   zc = 1 zm = 8 zs = 2 f = 0   zc = 9 zm = 8 zs = 3 f = 0   zc = 9 zm = 8 zs = 0 f = 5   zc = 9 zm = 8 zs = 1 f = 5   zc = 1 zm = 8 zs = 2 f = 5   zc = 9 zm = 8 zs = 3 f = 5                                 Selecting parameters:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7144 Output IDAT size = 7144 bytes (3026 bytes decrease) Output file size = 7222 bytes (3038 bytes = 29.61% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang/dotwhisker.Rcheck/vign_test/dotwhisker/vignettes/dotwhisker-vignette_files/figure-html/regularExpression-1.png 288x288 pixels, 8 bits/pixel, 242 colors in palette Input IDAT size = 2369 bytes Input file size = 3185 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 1694   zc = 9 zm = 8 zs = 1 f = 0   zc = 1 zm = 8 zs = 2 f = 0   zc = 9 zm = 8 zs = 3 f = 0   zc = 9 zm = 8 zs = 0 f = 5   zc = 9 zm = 8 zs = 1 f = 5   zc = 1 zm = 8 zs = 2 f = 5   zc = 9 zm = 8 zs = 3 f = 5                                 Selecting parameters:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 1694 Output IDAT size = 1694 bytes (675 bytes decrease) Output file size = 2510 bytes (675 bytes = 21.19% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang/dotwhisker.Rcheck/vign_test/dotwhisker/vignettes/dotwhisker-vignette_files/figure-html/relabel-1.png 288x288 pixels, 8 bits/pixel, 228 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 3354 bytes Input file size = 4128 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 2995   zc = 9 zm = 8 zs = 1 f = 0   zc = 1 zm = 8 zs = 2 f = 0   zc = 9 zm = 8 zs = 3 f = 0   zc = 9 zm = 8 zs = 0 f = 5   zc = 9 zm = 8 zs = 1 f = 5   zc = 1 zm = 8 zs = 2 f = 5   zc = 9 zm = 8 zs = 3 f = 5                                 Selecting parameters:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 2995 Output IDAT size = 2995 bytes (359 bytes decrease) Output file size = 3073 bytes (1055 bytes = 25.56% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang/dotwhisker.Rcheck/vign_test/dotwhisker/vignettes/dotwhisker-vignette_files/figure-html/custom-1.png 288x288 pixels, 8 bits/pixel, 232 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 3399 bytes Input file size = 4185 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 3045   zc = 9 zm = 8 zs = 1 f = 0   zc = 1 zm = 8 zs = 2 f = 0   zc = 9 zm = 8 zs = 3 f = 0   zc = 9 zm = 8 zs = 0 f = 5   zc = 9 zm = 8 zs = 1 f = 5   zc = 1 zm = 8 zs = 2 f = 5   zc = 9 zm = 8 zs = 3 f = 5                                 Selecting parameters:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 3045 Output IDAT size = 3045 bytes (354 bytes decrease) Output file size = 3123 bytes (1062 bytes = 25.38% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang/dotwhisker.Rcheck/vign_test/dotwhisker/vignettes/dotwhisker-vignette_files/figure-html/clm-1.png 288x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 4908 bytes Input file size = 4986 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 3659   zc = 9 zm = 8 zs = 1 f = 0   zc = 1 zm = 8 zs = 2 f = 0   zc = 9 zm = 8 zs = 3 f = 0   zc = 9 zm = 8 zs = 0 f = 5   zc = 9 zm = 8 zs = 1 f = 5   zc = 1 zm = 8 zs = 2 f = 5   zc = 9 zm = 8 zs = 3 f = 5                                 Selecting parameters:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 3659 Output IDAT size = 3659 bytes (1249 bytes decrease) Output file size = 3737 bytes (1249 bytes = 25.05% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang/dotwhisker.Rcheck/vign_test/dotwhisker/vignettes/dotwhisker-vignette_files/figure-html/by2sd-1.png 288x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 5566 bytes Input file size = 5644 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 4018   zc = 9 zm = 8 zs = 1 f = 0   zc = 1 zm = 8 zs = 2 f = 0   zc = 9 zm = 8 zs = 3 f = 0   zc = 9 zm = 8 zs = 0 f = 5   zc = 9 zm = 8 zs = 1 f = 5   zc = 1 zm = 8 zs = 2 f = 5   zc = 9 zm = 8 zs = 3 f = 5                                 Selecting parameters:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 4018 Output IDAT size = 4018 bytes (1548 bytes decrease) Output file size = 4096 bytes (1548 bytes = 27.43% decrease) Quitting from lines 273-308 [brackets] (dotwhisker-vignette.Rmd) Error: processing vignette 'dotwhisker-vignette.Rmd' failed with diagnostics: 'from' must be a finite number --- failed re-building ‘dotwhisker-vignette.Rmd’ --- re-building ‘kl2007_examples.Rmd’ using rmarkdown ** Processing: /data/gannet/ripley/R/packages/tests-clang/dotwhisker.Rcheck/vign_test/dotwhisker/vignettes/kl2007_examples_files/figure-html/unnamed-chunk-2-1.png 672x672 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 21601 bytes Input file size = 22483 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 20040   zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 19876   zc = 1 zm = 8 zs = 2 f = 0   zc = 9 zm = 8 zs = 3 f = 0   zc = 9 zm = 8 zs = 0 f = 5   zc = 9 zm = 8 zs = 1 f = 5   zc = 1 zm = 8 zs = 2 f = 5   zc = 9 zm = 8 zs = 3 f = 5                                 Selecting parameters:   zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 19876 Output IDAT size = 19876 bytes (1725 bytes decrease) Output file size = 19954 bytes (2529 bytes = 11.25% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang/dotwhisker.Rcheck/vign_test/dotwhisker/vignettes/kl2007_examples_files/figure-html/unnamed-chunk-3-1.png 672x672 pixels, 3x8 bits/pixel, RGB Input IDAT size = 48792 bytes Input file size = 48930 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 38149   zc = 9 zm = 8 zs = 1 f = 0   zc = 1 zm = 8 zs = 2 f = 0   zc = 9 zm = 8 zs = 3 f = 0   zc = 9 zm = 8 zs = 0 f = 5   zc = 9 zm = 8 zs = 1 f = 5   zc = 1 zm = 8 zs = 2 f = 5   zc = 9 zm = 8 zs = 3 f = 5                                 Selecting parameters:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 38149 Output IDAT size = 38149 bytes (10643 bytes decrease) Output file size = 38227 bytes (10703 bytes = 21.87% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang/dotwhisker.Rcheck/vign_test/dotwhisker/vignettes/kl2007_examples_files/figure-html/unnamed-chunk-4-1.png 672x768 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 26211 bytes Input file size = 27105 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 24057   zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 24030   zc = 1 zm = 8 zs = 2 f = 0   zc = 9 zm = 8 zs = 3 f = 0   zc = 9 zm = 8 zs = 0 f = 5   zc = 9 zm = 8 zs = 1 f = 5   zc = 1 zm = 8 zs = 2 f = 5   zc = 9 zm = 8 zs = 3 f = 5                                 Selecting parameters:   zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 24030 Output IDAT size = 24030 bytes (2181 bytes decrease) Output file size = 24108 bytes (2997 bytes = 11.06% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang/dotwhisker.Rcheck/vign_test/dotwhisker/vignettes/kl2007_examples_files/figure-html/unnamed-chunk-5-1.png 672x768 pixels, 3x8 bits/pixel, RGB Input IDAT size = 61554 bytes Input file size = 61716 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 47315   zc = 9 zm = 8 zs = 1 f = 0   zc = 1 zm = 8 zs = 2 f = 0   zc = 9 zm = 8 zs = 3 f = 0   zc = 9 zm = 8 zs = 0 f = 5   zc = 9 zm = 8 zs = 1 f = 5   zc = 1 zm = 8 zs = 2 f = 5   zc = 9 zm = 8 zs = 3 f = 5                                 Selecting parameters:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 47315 Output IDAT size = 47315 bytes (14239 bytes decrease) Output file size = 47393 bytes (14323 bytes = 23.21% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang/dotwhisker.Rcheck/vign_test/dotwhisker/vignettes/kl2007_examples_files/figure-html/unnamed-chunk-6-1.png 480x864 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 26191 bytes Input file size = 27085 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 24023   zc = 9 zm = 8 zs = 1 f = 0   zc = 1 zm = 8 zs = 2 f = 0   zc = 9 zm = 8 zs = 3 f = 0   zc = 9 zm = 8 zs = 0 f = 5   zc = 9 zm = 8 zs = 1 f = 5   zc = 1 zm = 8 zs = 2 f = 5   zc = 9 zm = 8 zs = 3 f = 5                                 Selecting parameters:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 24023 Output IDAT size = 24023 bytes (2168 bytes decrease) Output file size = 24101 bytes (2984 bytes = 11.02% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang/dotwhisker.Rcheck/vign_test/dotwhisker/vignettes/kl2007_examples_files/figure-html/unnamed-chunk-7-1.png 384x864 pixels, 3x8 bits/pixel, RGB Input IDAT size = 65710 bytes Input file size = 65884 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 47756   zc = 9 zm = 8 zs = 1 f = 0   zc = 1 zm = 8 zs = 2 f = 0   zc = 9 zm = 8 zs = 3 f = 0   zc = 9 zm = 8 zs = 0 f = 5   zc = 9 zm = 8 zs = 1 f = 5   zc = 1 zm = 8 zs = 2 f = 5   zc = 9 zm = 8 zs = 3 f = 5                                 Selecting parameters:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 47756 Output IDAT size = 47756 bytes (17954 bytes decrease) Output file size = 47834 bytes (18050 bytes = 27.40% decrease) --- finished re-building ‘kl2007_examples.Rmd’ SUMMARY: processing the following file failed:   ‘dotwhisker-vignette.Rmd’ Error: Vignette re-building failed. Execution halted
• checking PDF version of manual ... [10s/34s] OK
• checking HTML version of manual ... OK
• checking for non-standard things in the check directory ... OK
• checking for detritus in the temp directory ... OK
• DONE

Status: 2 ERRORs